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Jiang T, Liu R, Shen J. CRISPR dual enzyme cleavage triggers DNA and RNA substrate cleavage for SARS-CoV-2 dual gene detection. J Med Virol 2023; 95:e29090. [PMID: 37695079 DOI: 10.1002/jmv.29090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
The widespread dissemination of coronavirus 2019 imposes a significant burden on society. Therefore, rapid detection facilitates the reduction of transmission risk. In this study, we proposed a multiplex diagnostic platform for the rapid, ultrasensitive, visual, and simultaneous detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) open reading frame 1ab (ORF1ab) and N genes. A visual diagnostic method was developed using a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas12a/Cas13a dual-enzyme digestion system integrated with multiplex reverse transcriptase-recombinase polymerase amplification (RT-RPA). Two CRISPR-Cas proteins (Cas12a and Cas13a) were introduced into the system to recognize and cleave the N gene and ORF1ab gene, respectively. We used fluorescent or CRISPR double digestion test strips to detect the digested products, with the N gene corresponding to the FAM channel in the PCR instrument or the T1 line on the test strip, and the ORF1ab gene corresponding to the ROX channel in the PCR instrument or the T2 line on the test strip. The analysis can be completed in less than 20 min. Meanwhile, we assessed the application of the platform and determined a sensitivity of up to 200 copies/mL. Additionally, dual gene validation in 105 clinical nasopharyngeal swab samples showed a 100% positive predictive value agreement and a 95.7% negative predictive value agreement between our method and quantitative reverse transcription-polymerase chain reaction. Overall, our method offered a novel insight into the rapid diagnosis of SARS-CoV-2.
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Affiliation(s)
- Tong Jiang
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Runde Liu
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Jilu Shen
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Public Health Clinical Center, Hefei, Anhui, China
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Wang Y, Li X, Xu J, Zhou Q. A complete blood count-based multivariate model for predicting the recovery of patients with moderate COVID-19: a retrospective study. Sci Rep 2022; 12:18262. [PMID: 36309538 PMCID: PMC9617603 DOI: 10.1038/s41598-022-23285-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/27/2022] [Indexed: 12/31/2022] Open
Abstract
Many resource-limited countries need an efficient and convenient method to assess disease progression in patients with coronavirus disease 2019 (COVID-19). This study developed and validated a complete blood count-based multivariate model for predicting the recovery of patients with moderate COVID-19. We collected the clinical data and laboratory test results of 86 patients with moderate COVID-19. These data were categorized into two subgroups depending on the laboratory test time. Univariate logistic regression and covariance diagnosis were used to screen for independent factors, and multifactorial logistic regression was used for model building. Data from 38 patients at another hospital were collected for external verification of the model. Basophils (OR 6.372; 95% CI 3.284-12.363), mean corpuscular volume (OR 1.244; 95% CI 1.088-1.422), red blood cell distribution width (OR 2.585; 95% CI 1.261-5.297), and platelet distribution width (OR 1.559; 95% CI 1.154-2.108) could be combined to predict recovery of patients with moderate COVID-19. The ROC curve showed that the model has good discrimination. The calibration curve showed that the model was well-fitted. The DCA showed that the model is clinically useful. Small increases in the above parameters within the normal range suggest an improvement in patients with moderate COVID-19.
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Affiliation(s)
- Yiting Wang
- grid.430605.40000 0004 1758 4110Department of Laboratory Medicine, First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021 China
| | - Xuewen Li
- grid.430605.40000 0004 1758 4110Department of Laboratory Medicine, First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021 China
| | - Jiancheng Xu
- grid.430605.40000 0004 1758 4110Department of Laboratory Medicine, First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021 China
| | - Qi Zhou
- grid.430605.40000 0004 1758 4110Department of Pediatrics, First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021 China
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Li H, Zhu M, Zhang P, Yan X, Niu J, Wang Z, Cao J. Milder symptoms and shorter course in patients with re-positive COVID-19: A cohort of 180 patients from Northeast China. Front Microbiol 2022; 13:989879. [PMID: 36304945 PMCID: PMC9593080 DOI: 10.3389/fmicb.2022.989879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/07/2022] [Indexed: 01/08/2023] Open
Abstract
China experienced another widespread Coronavirus disease 2019 (COVID-19) outbreak recently caused by the Omicron variant, which is less severe but far more contagious than the other COVID-19 variants, leading local governments to focus efforts on eliminating the spread of the disease. Previous studies showed that after “recovering” from the virus, some patients could re-test positive for COVID-19 with nucleic acid tests, challenging the control of disease spread. In this study, we aimed to analyze the clinical and laboratory characteristics of re-positive COVID-19 patients in Northeast China. We retrospectively analyzed data from confirmed reverse transcription polymerase chain reaction (RT-PCR) re-positive COVID-19 patients who were admitted to the First Hospital of Jilin University, Jilin Province, China, from March to June 2022. Detailed clinical symptoms, medical history, anti-Corona Virus (CoV) IgG and IgM levels, and CoV nucleic acid cycle threshold (Ct) values during the re-positive period were collected and analyzed. A total of 180 patients were included in this study, including 62 asymptomatic cases and 118 mild cases. The cohort included 113 men and 67 women, with an average age of 45.73 years. The median time between recovery from the virus and re-positivity was 13 days. Our results showed that the proportion of re-positive patients with symptoms was lower, and the nucleic acid test-positive duration was shorter during the re-positive period. Furthermore, in patients with underlying disease, the proportion of patients with symptoms was higher, anti-CoV IgG levels were lower, and the total disease duration was longer. In conclusion, during the re-positive period, the symptoms were milder, and the CoV nucleic acid test-positive course was shorter. The concomitant underlying disease is an important factor associated with clinical symptoms, and the overall course of COVID-19 re-positive patients may be associated with lower anti-CoV IgG levels. Large-scale and multicenter studies are recommended to better understand the pathophysiology of recurrence in patients with COVID-19.
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Affiliation(s)
- Hongyan Li
- Department of Nursing, The First Hospital of Jilin University, Changchun, China
| | - Mingqin Zhu
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Peng Zhang
- Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Xingjian Yan
- Department of Urology, The First Hospital of Jilin University, Changchun, China
| | - Junqi Niu
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory of Zoonotic Disease, Department of Hepatology, Center of Infectious Disease and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
| | - Zhenyu Wang
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, China
- *Correspondence: Zhenyu Wang,
| | - Jie Cao
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
- Jie Cao,
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Peng Y, Wang S, Chai R, Chen Y, Li N, Zeng B, Tang Q, Zheng K, Liang Y, Xie S, Huang W, Wang S, Wang X. Clinical and Gene Features of SARS-CoV-2-Positive Recurrence in Patients Recovered From COVID-19. Front Mol Biosci 2022; 9:875418. [PMID: 35755819 PMCID: PMC9217101 DOI: 10.3389/fmolb.2022.875418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023] Open
Abstract
There are still frequent reports that a number of recovered coronavirus disease 2019 (COVID-19) patients following discharge have re-detectable positive (RP) results by RT-PCR. Understanding the clinical and molecular characteristics of RP patients may have implications for curbing the COVID-19 pandemic. In this study, 318 COVID-19 convalescent patients, including 59 RP patients and 259 non-RP (NRP) patients, were enrolled. Among RP patients, women accounted for a significantly high proportion (67.8%), and the titers of IgG and IgM antibodies in this group were also significantly high. Differentially expressed genes (DEGs), including 692 upregulated and 383 downregulated genes, overlapped in two public GEO datasets containing RP and NRP blood cell samples. Enrichment analysis indicated that these DEGs were related to several key signaling pathways, such as viral infection, immune activation, and inflammatory responses. Importantly, 59 indicator genes constituting the core network exhibited high diagnostic values and were correlated with markers of different immune cells. Among these, 12 drug-related genes were associated with the RP results. Our work suggests that, in addition to clinically available features, blood cell transcriptome sequencing can be performed to obtain gene signatures for diagnosis of RP patients.
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Affiliation(s)
- Yuying Peng
- Department of Pharmacy, Shenzhen Key Laboratory of Prevention and Treatment of Severe Infection, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.,School of Pharmacy, Jinan University, Guangzhou, China
| | - Shaoqi Wang
- Department of Internal Medicine, Hubei Province Corps Hospital of The Chinese Armed Police Force (CAPF), Wuhan, China
| | - Ruihuan Chai
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Yong Chen
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Nan Li
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Boning Zeng
- Department of Pharmacy, Shenzhen Key Laboratory of Prevention and Treatment of Severe Infection, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Qian Tang
- Department of Pharmacy, Shenzhen Key Laboratory of Prevention and Treatment of Severe Infection, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.,School of Pharmacy, Jinan University, Guangzhou, China
| | - Kai Zheng
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Youfang Liang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Shouxia Xie
- Department of Pharmacy, Shenzhen Key Laboratory of Prevention and Treatment of Severe Infection, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Wei Huang
- Bacteriology and Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Shaoxiang Wang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Xiao Wang
- Department of Pharmacy, Shenzhen Key Laboratory of Prevention and Treatment of Severe Infection, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.,School of Pharmacy, Jinan University, Guangzhou, China
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Yan Y, Yang L, Li X, Hao J, Wang B, Wang D, Wang J. Clinical Characteristics in Patients with Redetected Positive RNA Test After Recovery from Foreign-Imported COVID-19 Cases in Xi’an, China. Infect Drug Resist 2022; 15:3295-3307. [PMID: 35774303 PMCID: PMC9239575 DOI: 10.2147/idr.s371088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
Purpose At present, it has been found that managing patients with a redetected positive RNA test after recovery from foreign-imported coronavirus disease 2019 (COVID-19) cases in China is challenging. The purpose of the current study was to describe the clinical characteristics of these patients. Methods This retrospective cohort study included 137 COVID-19 patients who were discharged from the Xi’an Public Health Center from 28 July 2020 to 31 December 2021. We compared the clinical characteristics between positive retest patients and non-positive retest patients. Results 137 COVID-19 patients entered our study, 27 (19.7%) cases of COVID-19 with a redetected positive RNA test by the end of the follow-up period. Fever [(n = 31 (22.6%)], cough [n = 26 (18.9%)] and sore throat [n = 20 (14.5%)] were the most common initial symptoms among the foreign-imported COVID-19 patients, and there were almost no significant differences in initial symptoms between positive retest patients and non-positive retest patients. The positive retest patients had a higher lymphocyte count (p = 0.031) and lymphocyte percentage (p = 0.007) during readmission. There were generally no significant differences in other routine blood test findings, IgG and IgM antibody responses, between positive retest patients and non-positive retest patients, or in positive retest patients over time (before, during, or after positive patient detection). After readmission, positive retest patients displayed fewer symptoms or no obvious disease progression and more sustained remission by CT imaging. Conclusion Our findings revealed that the clinical characteristics at the time of initial diagnosis were not closely related to redetected positive RNA tests after recovery from foreign-imported COVID-19 cases. Positive retest patients had virtually no symptoms and displayed no obvious disease progression during readmission. These findings provide important information and clinical evidence for the effective management of foreign-imported COVID-19 patients during their convalescent phase.
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Affiliation(s)
- Yun Yan
- Department of Orthopedics and Traumatology, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, 710054, People’s Republic of China
| | - Lei Yang
- Department of Osteoporosis, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, 710054, People’s Republic of China
| | - Xiaoli Li
- Department of Respiratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, 710054, People’s Republic of China
| | - Jian Hao
- Xi’an Public Health Center, Xi’an, Shaanxi, 710200, People’s Republic of China
| | - Bijue Wang
- Xi’an Public Health Center, Xi’an, Shaanxi, 710200, People’s Republic of China
| | - Dan Wang
- Department of Pathology, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, 710054, People’s Republic of China
| | - Junning Wang
- Department of Respiratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, 710054, People’s Republic of China
- Correspondence: Junning Wang, Department of Respiratory, Honghui Hospital, Xi’an Jiaotong University, No. 555, Youyi East Road, Nanshaomen, Xi’an, Shaanxi, 710054, People’s Republic of China, Tel/Fax +86 02962818354, Email
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